Publications

Are you planning to publish a paper involving microscopy ?

You have the possibility to contact the microscopists and/or image analysts in our facility.

The BIOP staff is happy to guide you into following the FAIR principles and provide feedback about your Image Acquisition, Processing, Analysis and Visualization.

Furthermore the BIOP staff can :

  1. Assist in the production of Materials and Methods sections regarding microscopy and image processing.
  2. Advise on data and code accessibility and sharing.
  3. Provide feedback on best practices for data visualization.
  4. Advise on how to share data and code online ( Copyrighting, licensing, uploading ).

Moreover, this provides the BIOP with useful insights how its tools and services have contributed to the scientific literature.

How to acknowledge the BIOP in a publication?

The type of acknowledgement depends on the type of work and collaboration we have undertaken. For publications the rules and recommendations layed out in the EPFL compliance guide apply. 

For contributions to a publication which do not fulfill the criteria above, we recommend the following sentence:  

We would like to thank the EPFL BioImaging & Optics Core Facility and in particular [person(s)] for their assistance in [imaging / image processing].

It has been reported recently [1] that imaging methods are often not properly documented in publications.
In case you have a general question regarding Image acquisition, processing, analysis and visualization, or are unsure what to include into your Materials and Methods section, do not hesitate to drop us a line or pass by. We are happy to:

  1. Assist in the production of Materials and Methods sections regarding microscopy and image processing.
  2. Advise on data and code accessibility and sharing.
  3. Provide feedback on best practices for data visualization.
  4. Advise on how to share data and code online ( Copyrighting, licensing, uploading ).

[1]  Marqués et al.: Science Forum: Imaging methods are vastly underreported in biomedical research, eLife 2020;9:e55133, doi: 10.7554/eLife.55133, Aug 11, 2020.


Latest Publications

Below you will find recent publications by all members of the BioImaging & Optics Platform.

To find all publications, you may head to InfoScience.

An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix

N. Chiaruttini; O. Burri; P. Haub; R. Guiet; J. Sordet-Dessimoz et al. 

Frontiers In Computer Science. 2022-01-05. Vol. 3, p. 780026. DOI : 10.3389/fcomp.2021.780026.

BigDataProcessor2: a free and open-source Fiji plugin for inspection and processing of TB sized image data

C. Tischer; A. Ravindran; S. Reither; N. Chiaruttini; R. Pepperkok et al. 

Bioinformatics. 2021-09-15. Vol. 37, num. 18, p. 3079-3081. DOI : 10.1093/bioinformatics/btab106.

QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

G. Nelson; U. Boehm; S. Bagley; P. Bajcsy; J. Bischof et al. 

Journal Of Microscopy. 2021-08-11. DOI : 10.1111/jmi.13041.

Miniature neurotransmission is required to maintain Drosophila synaptic structures during ageing

S. Banerjee; S. Vernon; W. Jiao; B. J. Choi; E. Ruchti et al. 

Nature Communications. 2021-07-20. Vol. 12, num. 1, p. 4399. DOI : 10.1038/s41467-021-24490-1.

QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

U. Boehm; G. Nelson; C. M. Brown; S. Bagley; P. Bajcsy et al. 

Nature Methods. 2021-05-21. DOI : 10.1038/s41592-021-01162-y.

Capturing Cardiogenesis in Gastruloids

G. Rossi; N. Broguiere; M. Miyamoto; A. Boni; R. Guiet et al. 

Cell Stem Cell. 2021-02-04. Vol. 28, num. 2, p. 230-+. DOI : 10.1016/j.stem.2020.10.013.

Biotin-NeutrAvidin Mediated Immobilization of Polymer Micro- and Nanoparticles on T Lymphocytes

M. Ayer; O. Burri; R. Guiet; A. Seitz; E. Kaba et al. 

Bioconjugate Chemistry. 2021-03-17. Vol. 32, num. 3, p. 541-552. DOI : 10.1021/acs.bioconjchem.1c00026.

MarrowQuant across Aging and Aplasia: A Digital Pathology Tool for Quantification of Bone Marrow Compartments in Histological Sections

J. Tratwal; I. Bekri; C. Boussema; N. Kunz; R. Sarkis et al. 

2020-11-01. Annual Meeting of the American-Society-for-Bone-and Mineral Research (ASBMR), ELECTR NETWORK, Sep 11-15, 2020. p. 95-95.

T Cell-Mediated Transport of Polymer Nanoparticles across the Blood-Brain Barrier

M. Ayer; M. Schuster; I. Gruber; C. Blatti; E. Kaba et al. 

Advanced Healthcare Materials. 2020-11-25.  p. 2001375. DOI : 10.1002/adhm.202001375.

Hookworms Evade Host Immunity by Secreting a Deoxyribonuclease to Degrade Neutrophil Extracellular Traps

T. Bouchery; M. Moyat; J. Sotillo; S. Silverstein; B. Volpe et al. 

Cell Host & Microbe. 2020-02-12. Vol. 27, num. 2, p. 277-+. DOI : 10.1016/j.chom.2020.01.011.

Conference Posters

You can find our conference posters here in PDF format

ELMI 2017

ELMI 2016